Launched in 1986, the Annapurna Conservation Area Project (ACAP) is the largest undertaking of NTNC. It is also the first Conservation Area and largest Protected Area in Nepal. It covers an area of 7,629 sq. km. and is home to over 100,000 residents of different cultural and linguistic groups.

With the successful experience of Integrated Conservation and Development Programme (ICDP) in ACAP, NTNC started working in the Manaslu region from the beginning of 1997 as the Manaslu Ecotourism Development Project with funding support of the Government of Nepal and the Asian Development Bank under the Ministry of Culture, Tourism and Civil Aviation’s Second Tourism Infrastructure Development

The Government of Nepal, through a Nepal Gazette notice dated July 19, 2010 (Section 60, Number 14, Part 5, 2067/04/03 B.S.), has entrusted the management responsibility of Gaurishankar Conservation Area to the National Trust for Nature Conservation (NTNC) for 20 years.

In 1989, after Smithsonian Institution,USA completed its assignment in the Chitwan National Park (CNP), Nepal and handed over the Nepal Terai Ecology Project to NTNC, the Trust established the Nepal Conservation Research and Training Center (NCRTC) to conduct biological research and monitoring of flora and fauna in the lowland (Terai) protected areas of Nepal.

NTNC started its conservation activities, mainly wildlife research and monitoring, in the Shuklaphanta National Park (ShNP) in 1999. Regular activities are being carried out since 2002. The main objective of the Shuklaphanta Conservation Program (SCP) is to monitor and conduct research on the natural resources.

Koshi Conservation Center (KCC) is NTNC's eight and most recent project under operation. It was set up as independent project officially from September 2021. Prior to that, the Trust's Koshi-related operations were managed from its Biodiversity Conservation Center (NTNC-BCC) office in Sauraha, Chitwan.